Mercurial > repos > tiagoantao > clone_filter
diff STACKS_clone_filter.py @ 0:42e64fbf4609 draft
planemo upload commit 60a090d1dc89c2eb383feeb35cd6078b9130e0e5-dirty
author | tiagoantao |
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date | Tue, 02 Feb 2016 21:15:50 -0500 |
parents | |
children | 1a5ebb16aaea |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/STACKS_clone_filter.py Tue Feb 02 21:15:50 2016 -0500 @@ -0,0 +1,48 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- + +import shutil +import subprocess +import argparse + + +def __main__(): + parser = argparse.ArgumentParser() + parser.add_argument('-f', type=str) + parser.add_argument('-fwd', type=str) + parser.add_argument('-rev', type=str) + + #parser.add_argument('-k', action='store_true') + + options = parser.parse_args() + + # create the working dir + os.mkdir('job_outputs') + os.chdir('job_outputs') + + # STACKS_archive + # check if zipped files are into the tab + extract_compress_files(options.P, os.getcwd()) + + # create the populations command input line + cmd_line=['clone_filter'] + if options.f is not None: + cmd_line.extend(['-f', options.f]) + else: + cmd_line.extend(['-1', options.fwd]) + cmd_line.extend(['-2', options.rev]) + + print "[CMD]:"+' '.join(cmd_line) + subprocess.call(cmd_line) + + # postprocesses + clean_files = glob.glob('*.fq') + if options.f is not None: + shutil.copy(clean_files[0], 'clean.fq') + else: + shutil.copy(clean_files[0], 'fwd.fq') + shutil.copy(clean_files[1], 'rev.fq') + + +if __name__ == '__main__': + __main__()